4 Answers
4

A couple of popular options that haven't been mentioned by others are OSSEC and Verisys.

OSSEC is an Open Source system that can monitor filesystems for changes. It's certainly not the slickest in terms of ease of use, but it is free, and works on Windows and Linux.

Ionx Verisys is a commercial file integrity monitoring system. This is much easier to use than OSSEC, or Tripwire (which someone else already mentioned), and isn't that expensive compared to other commercial alternatives (e.g Tripwire). Though it's more expensive than OSSEC, of course :)